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--- exercises:2015_ethz_mmm:alanine_modify [2015/02/27 09:04] – yakutovich
+++ exercises:2015_ethz_mmm:alanine_modify [2015/03/19 22:16] – yakutovich
@@ Line 1: / Line 1: @@
 ====== Modification of the dihedral parameters ======
+<note warning>
+TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
+you@eulerX ~$ module load courses mmm ; mmm-init
+</note>
 Download the 2.3 exercise into your $HOME folder and unzip it.
@@ Line 31: / Line 36: @@
 Use m_pdbtorsion to measure the angles, but don't forget to load library in the memory first:
 <code>
-you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash
+you@eulerX exercise_2.3$ . ~/Scripts/myfunctions.bash
 </code>
 </note>
-To get help how to use the program simply type its name without any argument, and press "Enter"
+To get help how to use the program simply type its name without any argument, and press "Enter":
 <code>
 you@eulerX exercise_2.3$ m_pdbtorsion
 </code>
+<note>
+Hint: Definition of **PHI** and **PSI** torsion angles for this particular system is the following...
+<code bash>
+PHI: 5 7 9 15
+PSI: 7 9 15 17
+</code>
+</note>
@@ Line 48: / Line 61: @@
 Run cp2k with:
 <code bash>
-you@eulerX $ bsub cp2k.popt -i inp.a -o out.a
+you@eulerX exercise_2.3$ bsub cp2k.popt -i inp.a -o out.a
 </code>
 The file a_opt-pos-1.pdb contains a row of configurations. To extract the last one:
 <code bash>
-you@eulerX $ tail -25  a_opt-pos-1.pdb > amin.pdb
+you@eulerX exercise_2.3$ tail -25  a_opt-pos-1.pdb > amin.pdb
 </code>
@@ Line 64: / Line 77: @@
 Check the final energies:
 <code bash>
-you@eulerX Minimum_a$ grep 'E =' a_opt-pos-1.pdb
+you@eulerX exercise_2.3$ grep 'E =' a_opt-pos-1.pdb
-you@eulerX Minimum_b$ grep 'E =' b_opt-pos-1.pdb
+you@eulerX exercise_2.3$ grep 'E =' b_opt-pos-1.pdb
 </code>
 Is the energy becoming lower during the optimization?
@@ Line 80: / Line 93: @@
 and submit a new job:
 <code>
-you@eulerX $ bsub < ff_modify
+you@eulerX exercise_2.3$ bsub < ff_modify
 </code>
 which will perform different jobs with the torsional term for the angle **PSI** modified by multiplication by 0.25, 0.5, 1, 2, 4. This corresponds to output lines enemul.*  with three columns : the restrained phi, psi, and the energy in Hartree.
@@ Line 88: / Line 101: @@
 In this way you will obtain energy profiles joining the two minima
 <note tip>
-Would it be an idea to do a nudged elastic band?
+Could you expain an idea how to setup a nudged elastic band simulation to study the reaction pathway from **A** to the **B** point?
+</note>
+  * The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load "mod_ff.gnu" from within gnuplot:
+<code gnuplot>
+you@eulerX exercise_2.3$ gnuplot
+gnuplot> load "mod_ff.gnu"
+</code>
+<note tip>
+How will the line profile change? Why?
 </note>
-  - The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential. Use this time the command "load "mod_ff.gnu" from within gnuplot.
-  - How will the line profile change? Why?